DUF3870 - PFAM28P - GREMLIN Contacts

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DUF3870 - Domain of unknown function (DUF3870)

PFAM:	PF12986	Sequences: YITGYAKLPQGNAATEVYKVFGIGLEVDRETGVIVDASCTLVTELTRDFVRSLLVGYNLLDGIEEIIEEIERRYFGSSQKALIVALKDAYKKYR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	94 (93)
Sequences:	1067 (825)
Seq/√Len:	85.6
META:	0.717

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_L	89_A	3.076	1.00
16_E	19_K	2.744	1.00
27_V	59_L	2.486	1.00
57_Y	69_E	2.438	1.00
48_D	52_S	2.364	1.00
88_D	91_K	2.347	1.00
36_D	51_R	2.216	1.00
1_Y	24_G	2.170	1.00
67_I	83_I	2.144	1.00
29_R	72_R	2.076	1.00
26_E	52_S	1.914	1.00
58_N	61_D	1.846	1.00
44_E	48_D	1.793	1.00
38_S	45_L	1.762	1.00
63_I	90_Y	1.742	1.00
66_I	86_L	1.730	1.00
32_G	58_N	1.721	1.00
57_Y	66_I	1.704	1.00
28_D	35_V	1.585	1.00
54_L	86_L	1.570	1.00
28_D	33_V	1.560	1.00
32_G	93_Y	1.527	1.00
68_E	71_E	1.462	0.99
67_I	71_E	1.460	0.99
11_G	16_E	1.428	0.99
43_T	46_T	1.426	0.99
44_E	47_R	1.389	0.99
38_S	47_R	1.384	0.99
36_D	48_D	1.314	0.99
62_G	90_Y	1.313	0.99
49_F	73_R	1.297	0.99
8_L	14_A	1.262	0.98
65_E	68_E	1.253	0.98
62_G	66_I	1.233	0.98
69_E	73_R	1.227	0.98
62_G	65_E	1.195	0.97
33_V	58_N	1.183	0.97
5_Y	22_G	1.176	0.97
57_Y	62_G	1.163	0.97
49_F	53_L	1.117	0.96
39_C	50_V	1.112	0.96
13_A	20_V	1.099	0.96
57_Y	65_E	1.090	0.96
61_D	65_E	1.083	0.95
41_L	46_T	1.079	0.95
26_E	35_V	1.072	0.95
22_G	40_T	1.062	0.95
33_V	56_G	1.048	0.95
40_T	43_T	1.009	0.93
29_R	73_R	0.996	0.93
54_L	74_Y	0.971	0.92
13_A	22_G	0.948	0.91
50_V	86_L	0.947	0.91
71_E	79_Q	0.923	0.90
50_V	54_L	0.902	0.89
5_Y	13_A	0.901	0.89
22_G	78_S	0.893	0.88
38_S	44_E	0.892	0.88
36_D	55_V	0.889	0.88
13_A	92_K	0.869	0.87
30_E	33_V	0.843	0.85
12_N	78_S	0.840	0.85
63_I	86_L	0.836	0.85
84_V	88_D	0.804	0.82
30_E	61_D	0.803	0.82
43_T	47_R	0.796	0.82
64_E	68_E	0.793	0.82
5_Y	43_T	0.792	0.81
70_I	79_Q	0.788	0.81
34_I	59_L	0.784	0.81
25_L	82_L	0.783	0.81
39_C	76_G	0.779	0.80
70_I	82_L	0.779	0.80
34_I	62_G	0.773	0.80
54_L	66_I	0.771	0.80
4_G	88_D	0.768	0.79
12_N	41_L	0.766	0.79
6_A	32_G	0.764	0.79
14_A	21_F	0.754	0.78
78_S	81_A	0.753	0.78
67_I	70_I	0.752	0.78
68_E	72_R	0.739	0.77
10_Q	74_Y	0.729	0.76
2_I	25_L	0.727	0.76
3_T	24_G	0.721	0.75
84_V	87_K	0.720	0.75
6_A	67_I	0.710	0.74
3_T	89_A	0.707	0.74
14_A	78_S	0.706	0.73
21_F	77_S	0.696	0.72
63_I	67_I	0.684	0.71
8_L	15_T	0.677	0.70
59_L	90_Y	0.672	0.70
30_E	69_E	0.672	0.70
50_V	82_L	0.664	0.69
26_E	36_D	0.662	0.69
8_L	12_N	0.660	0.68
14_A	22_G	0.660	0.68
19_K	69_E	0.647	0.67
8_L	81_A	0.646	0.67
70_I	86_L	0.640	0.66
60_L	90_Y	0.639	0.66
18_Y	74_Y	0.639	0.66
40_T	91_K	0.636	0.65
12_N	77_S	0.632	0.65
87_K	92_K	0.629	0.65
27_V	75_F	0.629	0.65
38_S	74_Y	0.622	0.64
29_R	32_G	0.619	0.63
68_E	90_Y	0.616	0.63
60_L	66_I	0.615	0.63
71_E	80_K	0.598	0.61
86_L	90_Y	0.594	0.60
81_A	85_A	0.594	0.60
15_T	19_K	0.593	0.60
48_D	51_R	0.584	0.59
5_Y	40_T	0.583	0.59
56_G	64_E	0.579	0.58
11_G	43_T	0.579	0.58
22_G	77_S	0.571	0.57
64_E	67_I	0.565	0.56
53_L	69_E	0.564	0.56
77_S	88_D	0.562	0.56
5_Y	12_N	0.554	0.55
51_R	72_R	0.549	0.54
31_T	58_N	0.548	0.54
13_A	76_G	0.545	0.54
76_G	87_K	0.545	0.54
39_C	43_T	0.532	0.52
30_E	51_R	0.531	0.52
59_L	74_Y	0.527	0.51
35_V	52_S	0.518	0.50
52_S	55_V	0.516	0.50
32_G	60_L	0.516	0.50
46_T	89_A	0.515	0.50
75_F	79_Q	0.514	0.50
83_I	93_Y	0.507	0.49
17_V	20_V	0.504	0.48
55_V	84_V	0.501	0.48
8_L	78_S	0.500	0.48

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
2z7eA	5	1	47.8	0.873	Contact Map
3r07C	1	0.8298	32.2	0.885	Contact Map
1su0B	1	0.9468	32.1	0.885	Contact Map
3fxgA	5	0.9894	30.2	0.887	Contact Map
4kn9L	2	0.7872	27.2	0.889	Contact Map
4eb5C	1	0.9787	23.3	0.893	Contact Map
3i6eA	4	0.8936	21.8	0.894	Contact Map
1xjsA	1	0.9681	21.4	0.894	Contact Map
1e3dB	1	0.8511	20.8	0.895	Contact Map
3i4kA	4	0.9894	19.5	0.896	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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